The 1st European Congress on Cell-Free Synthetic Biology, intends to bring together an interdisciplinary group of researchers from a broad range of scientific fields to
i) present the current state-of-the-art in cell-free synthetic biology,
ii) define the future direction of the field, and
iii) to serve as an environment for sharing ideas and engaging in new collaborations.
The 1st ECCSB will be hosted by the Congressi Stefano Franscini at the Conference Center Monte Verita in Ascona. Ascona is located on the northern end of Lago Maggiore in Switzerland.
Title of talk:
Modeling and characterization of cell-free implementations of RNA-based logic gates
RNAs are involved in a wide range of cellular regulatory functions and were recently shown to be a promising tool for controlling gene expression in synthetic circuits. Escherichia coli-based cell-free transcription translation (TX-TL) systems offers an appealing and robust alternative environment to the traditional lengthy in vivo test cycles for implementing such synthetic circuits of increasing complexity. We show first that certain parts can be studied and decoupled in a TX-only environment. Here, we use this method for demonstrating the use of a dual system mRNA reporter, allowing our subsequent RNA circuits to be fluorescently tracked with the iSpinach along with the Malachite green aptamer. We also investigate the use of the well characterized theophylline riboswitch in a translational regulated cascade. A down-scaled version of a microfluidic chemostat based on previously published designs are used for applying different signal patterning over a sustained period of time. The reactions are thus performed in continuous mode, and a systematic comparison is made against their counterpart ran in batch from circular or linear templates. Finally, the challenges of integrating other RNA regulators such as Small Transcripton Activators or Repressors (STAR) RNA to such synthetic circuits are presented and strategies to measure their combinatorial effects through the TX-TL environment are discussed. We use a derivative matching approach based on Gaussian processes and Bayesian inference to calibrate ODE models to the measure cell-free circuit dynamics.